Contacts of the helix formed by residues 390 - 413 (chain C) in PDB entry 3IFS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 390 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C MSE 5.5 0.2 - - - +
96C LEU* 3.6 12.4 - - - +
388C GLU* 3.3 34.8 + - + +
389C LEU* 1.3 75.0 - - - +
391C GLU* 1.3 67.1 + - - +
392C TYR* 3.6 9.6 + - - +
393C THR* 2.7 39.0 + - - -
394C PHE* 2.9 28.8 + - - +
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Residues in contact with GLU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C LEU* 4.0 15.7 - - + -
224C GLY 4.9 0.5 - - - +
225C LEU* 3.6 27.1 - - + +
226C ASN* 2.9 54.6 + - - +
229C GLU* 4.2 5.2 - - + +
230C MSE 3.4 22.2 - - + +
390C ASN* 1.3 79.0 - - - +
392C TYR* 1.3 68.1 + - - +
394C PHE* 3.2 3.8 + - - +
395C GLY 3.0 18.5 + - - -
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Residues in contact with TYR 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR* 5.1 13.2 - - - -
229C GLU* 3.3 34.7 + - + +
232C LYS* 3.8 14.1 - - + -
233C GLY* 3.3 38.0 - - - -
236C ALA* 3.2 20.5 - - + +
390C ASN* 3.4 10.4 + - - +
391C GLU* 1.3 78.5 - - - +
393C THR* 1.3 72.7 + - - +
395C GLY 3.2 2.4 + - - -
396C TYR* 3.0 31.4 + + + +
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Residues in contact with THR 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR 4.9 8.3 + - - +
5C VAL* 3.8 18.2 - - + -
386C ILE* 3.4 33.0 - - + -
387C PRO* 4.4 6.4 - - + +
388C GLU* 3.2 17.7 + - - +
389C LEU* 5.5 0.4 - - + -
390C ASN* 2.7 26.8 + - - -
392C TYR* 1.3 85.2 - - - +
394C PHE* 1.3 56.0 + - - +
396C TYR* 3.2 5.3 + - - +
397C LEU* 2.8 31.3 + - + +
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Residues in contact with PHE 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLY* 4.0 10.8 - - - -
91C ALA* 4.3 2.7 - - + -
92C ALA* 3.5 39.0 - - + -
95C MSE 3.8 28.7 - - + -
96C LEU* 4.1 10.8 - - + -
211C VAL* 4.3 13.7 - - + -
212C LEU* 5.0 1.6 - - + -
230C MSE 3.6 30.1 - - + -
281C PHE* 3.9 24.7 - + - -
284C TRP* 6.2 1.8 - + - -
390C ASN 2.9 14.6 + - - +
391C GLU* 3.2 7.4 + - - +
393C THR* 1.3 74.9 - - - +
395C GLY* 1.3 58.0 + - - +
397C LEU* 3.4 6.3 + - - +
398C VAL* 2.9 51.4 + - + +
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Residues in contact with GLY 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LEU* 5.0 2.7 - - - -
230C MSE 3.4 29.8 - - - -
234C ALA* 3.5 20.9 - - - +
391C GLU 3.0 10.5 + - - -
392C TYR 3.2 1.5 + - - -
394C PHE* 1.3 76.2 - - - +
396C TYR* 1.3 65.5 + - - +
398C VAL* 3.5 4.7 + - - +
399C TYR 3.1 17.7 + - - -
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Residues in contact with TYR 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR 6.1 0.2 - - - -
4C HIS* 3.0 21.9 - + - -
5C VAL* 3.6 42.3 + - + -
233C GLY* 3.4 24.0 - - - +
234C ALA* 4.4 0.7 - - - +
236C ALA* 3.8 12.3 - - + -
237C GLY* 3.6 17.5 - - - -
240C ASP* 2.8 33.7 + - - +
241C PHE* 3.6 28.8 - + - -
392C TYR* 3.0 21.8 + + + +
393C THR* 3.5 11.9 - - - +
395C GLY* 1.3 74.8 - - - +
397C LEU* 1.3 56.9 + - - +
399C TYR* 3.3 5.5 + - - +
400C PHE* 2.9 25.6 + - + +
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Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 4.1 16.4 - - + +
95C MSE 4.7 13.2 - - + -
281C PHE* 3.7 33.7 - - + -
330C LEU* 5.0 0.7 - - + -
384C VAL* 4.0 22.0 - - + -
386C ILE* 3.6 31.9 - - + -
393C THR* 2.8 20.8 + - + +
394C PHE* 3.7 6.1 - - - +
396C TYR* 1.3 72.2 - - - +
398C VAL* 1.3 64.6 + - - +
400C PHE* 3.3 7.7 + - + +
401C PHE* 3.1 49.7 + - + -
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C VAL* 3.8 18.6 - - + -
212C LEU* 4.1 14.6 - - + -
281C PHE* 4.3 6.7 - - + -
284C TRP* 3.8 22.7 - - + -
394C PHE* 2.9 54.7 + - + +
395C GLY* 3.7 4.5 - - - +
397C LEU* 1.3 75.3 - - - +
399C TYR* 1.3 59.1 + - - +
401C PHE 3.4 1.4 + - - -
402C GLU* 2.9 57.9 + - - +
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C HIS* 5.3 0.3 - - - -
48C TRP* 3.7 19.5 - + - -
49C VAL* 2.7 44.1 + - - +
52C PRO* 3.8 22.4 - - + -
212C LEU* 5.3 2.0 - - + -
234C ALA* 3.9 13.9 - - + +
237C GLY* 3.6 9.9 - - - -
238C ARG* 3.4 36.1 + - + +
241C PHE* 4.1 5.4 - + + -
395C GLY 3.1 15.5 + - - +
396C TYR 3.7 3.8 - - - +
398C VAL* 1.3 77.1 - - + +
400C PHE* 1.3 66.2 + - - +
402C GLU* 3.8 13.4 - - - +
403C LYS* 2.9 50.4 + - + +
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Residues in contact with PHE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 5.0 9.2 - - + -
6C THR 5.7 0.2 - - - -
7C PHE* 4.1 18.8 - + + -
241C PHE* 3.6 35.8 - + + -
250C PRO* 3.7 13.7 - - + -
251C ALA* 3.7 26.6 - - - +
254C TYR* 4.1 25.4 - + + -
384C VAL* 4.2 14.8 - - + -
396C TYR* 2.9 16.7 + - + +
397C LEU* 3.4 16.2 - - + +
399C TYR* 1.3 75.6 - - - +
401C PHE* 1.3 97.7 + + - +
403C LYS 3.6 0.2 + - - -
404C ALA* 3.0 29.3 + - - +
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Residues in contact with PHE 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 3.7 32.5 - + - -
271C LEU* 4.5 6.1 - - + -
281C PHE* 3.7 30.3 - + - -
284C TRP* 4.0 6.5 - + + -
285C TRP* 3.7 28.3 - + - -
288C LEU* 3.5 16.7 - - + +
289C PHE* 3.8 5.0 - + - -
328C THR* 5.2 0.2 - - + -
330C LEU* 4.0 20.0 - - + -
384C VAL* 4.3 7.0 - - + -
397C LEU* 3.1 40.4 + - + +
398C VAL 3.9 3.1 - - - +
400C PHE* 1.3 94.9 - + - +
402C GLU* 1.3 59.2 + - - +
404C ALA* 3.8 2.0 - - - +
405C CYS* 2.9 31.2 + - - +
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Residues in contact with GLU 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TRP* 3.6 31.8 - - + +
209C PHE* 3.6 53.8 - - + +
211C VAL* 4.3 4.3 - - - +
212C LEU* 5.1 5.4 - - - +
284C TRP* 4.1 17.0 - - + -
288C LEU* 4.0 8.3 - - + -
398C VAL* 2.9 41.3 + - - +
399C TYR* 3.8 15.1 - - - +
401C PHE* 1.3 75.2 - - - +
403C LYS* 1.3 63.3 + - - +
405C CYS* 3.2 3.3 + - - +
406C ALA 3.1 18.7 + - - -
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Residues in contact with LYS 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 4.1 0.2 + - - -
35C ILE* 4.4 11.6 - - + +
36C HIS* 3.0 32.3 + - - -
48C TRP* 4.0 21.3 - - + -
49C VAL* 4.3 5.8 - - - -
238C ARG 5.9 0.4 - - - -
241C PHE* 2.8 36.8 + - + +
251C ALA* 4.3 7.0 - - + -
252C TYR* 2.7 38.8 + - + +
399C TYR* 2.9 41.5 + - + +
400C PHE 4.1 2.5 - - - +
402C GLU* 1.3 76.8 - - - +
404C ALA* 1.3 63.3 + - - +
406C ALA* 3.4 3.6 + - - +
407C MSE 3.3 21.5 + - - +
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Residues in contact with ALA 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ALA* 3.3 30.7 - - + +
254C TYR* 3.7 27.4 - - + -
255C ALA* 3.5 5.6 - - - +
289C PHE* 4.5 0.7 - - - -
400C PHE* 3.0 20.7 + - + +
401C PHE* 3.8 5.2 - - - +
403C LYS* 1.3 75.5 - - - +
405C CYS* 1.3 58.8 + - - +
407C MSE 3.4 2.1 + - - -
408C SER* 2.9 31.8 + - - -
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Residues in contact with CYS 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 4.4 4.0 - - + -
288C LEU* 3.6 27.6 - - + -
289C PHE* 3.6 26.0 - - + -
292C SER* 3.2 39.0 - - - -
293C GLU* 4.5 1.9 - - - +
401C PHE 2.9 18.0 + - - +
402C GLU 3.2 5.6 + - - +
404C ALA* 1.3 76.0 - - - +
406C ALA* 1.3 61.8 + - - +
408C SER* 3.2 1.4 + - - -
409C GLY* 2.9 23.0 + - - -
416C PRO* 4.7 1.5 - - - +
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 4.0 15.7 - - + -
48C TRP* 3.8 26.9 - - + -
209C PHE* 5.2 0.4 - - - -
402C GLU 3.1 5.7 + - - -
403C LYS* 3.7 8.5 - - - +
404C ALA 3.3 0.2 - - - -
405C CYS* 1.3 77.0 - - - +
407C MSE 1.3 62.5 + - - +
409C GLY 3.4 0.2 + - - -
410C TYR* 3.1 30.2 + - - -
416C PRO* 3.8 6.5 - - - +
417C PHE* 3.8 25.1 - - + -
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Residues in contact with MSE 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL* 3.4 36.3 - - + +
31C THR* 3.6 23.1 - - + -
32C HIS* 3.8 12.3 - - - +
35C ILE* 4.2 7.3 - - + +
252C TYR* 3.6 52.5 - - + +
255C ALA* 3.7 16.2 - - + -
403C LYS 3.3 5.7 + - - +
404C ALA 3.7 6.7 - - - +
406C ALA* 1.3 78.6 - - - +
408C SER* 1.3 58.0 + - - +
410C TYR* 3.3 3.0 + - - -
411C LEU* 2.9 53.4 + - + +
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Residues in contact with SER 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ALA* 3.6 18.1 - - - +
258C ARG* 2.8 21.3 + - - -
259C ASN* 3.2 22.0 + - - +
289C PHE* 4.4 2.9 - - - -
293C GLU* 2.4 26.6 + - - +
404C ALA 2.9 18.6 + - - -
405C CYS* 3.6 6.3 - - - -
407C MSE 1.3 75.3 - - - +
409C GLY* 1.3 57.7 + - - +
411C LEU* 3.3 1.3 + - - -
412C LEU* 3.0 25.3 + - - +
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Residues in contact with GLY 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLU* 3.3 13.2 + - - -
405C CYS 2.9 16.0 + - - -
406C ALA 3.9 0.9 - - - -
408C SER* 1.3 77.7 - - - +
410C TYR* 1.3 60.5 + - - +
412C LEU* 3.3 2.1 + - - +
413C GLY 3.2 5.2 + - - -
414C VAL* 3.1 43.9 + - - +
416C PRO* 4.1 9.2 - - - -
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Residues in contact with TYR 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR 5.6 1.6 - - - +
24B LEU* 5.8 0.2 - - - +
31C THR* 3.5 34.3 + - + +
34C ALA* 5.3 4.9 + - + -
35C ILE* 3.8 26.0 - - + -
40C GLY* 3.7 15.4 + - - -
41C ALA* 2.5 44.5 + - + -
42C GLY 4.8 0.9 - - - -
43C ASN 4.9 0.2 + - - -
46C LEU* 5.0 6.1 - - + +
406C ALA 3.1 24.3 + - - +
407C MSE 3.8 0.7 - - - +
409C GLY* 1.3 77.3 - - - +
411C LEU* 1.3 61.7 + - - +
413C GLY* 3.2 13.0 + - - -
414C VAL 4.0 6.3 - - - -
416C PRO* 3.6 13.0 - - + +
417C PHE* 3.4 25.4 - + - -
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Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 6.1 0.2 - - - +
263B ASN* 5.6 0.7 + - - -
24C LEU* 4.3 18.2 - - + -
27C ALA* 4.4 19.3 - - + -
28C VAL* 4.3 4.0 - - + -
31C THR* 4.5 8.7 - - - +
255C ALA 4.4 4.0 - - - +
256C VAL* 3.8 35.2 - - + +
259C ASN* 4.1 13.9 - - + +
407C MSE 2.9 50.6 + - + +
408C SER 3.8 3.8 - - - +
409C GLY 3.3 0.2 - - - -
410C TYR* 1.3 76.9 - - - +
412C LEU* 1.3 61.1 + - - +
413C GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 5.4 0.5 - - - +
263B ASN* 3.7 30.7 + - + +
259C ASN* 3.6 17.7 + - - +
262C TYR* 3.8 30.3 - - + -
293C GLU* 3.9 39.7 - - + +
298C LYS* 4.3 12.3 + - + +
299C GLY* 4.1 14.1 - - - +
300C ILE 5.4 0.4 - - - +
408C SER 3.0 17.5 + - - +
409C GLY 3.5 5.8 - - - +
411C LEU* 1.3 76.5 - - - +
413C GLY* 1.3 59.2 + - - +
414C VAL* 4.0 16.2 - - + -
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Residues in contact with GLY 413 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 4.7 4.7 - - - -
23B TYR* 3.5 22.6 - - - +
24B LEU* 3.9 24.8 - - - +
296C ASP* 4.7 2.6 - - - +
298C LYS* 4.4 10.2 + - - -
409C GLY 3.2 2.6 + - - -
410C TYR 3.2 9.8 + - - -
411C LEU 3.2 4.0 - - - -
412C LEU* 1.3 79.6 - - - +
414C VAL* 1.3 65.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il